Liam-Research-2-Integration

library(tidyverse)

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-- Attaching packages ---------------------------------------------------------------------- tidyverse 1.3.1 --
√ ggplot2 3.3.5     √ purrr   0.3.4
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√ tidyr   1.2.0     √ stringr 1.4.0
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-- Conflicts ------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
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library(tuneR)
library(devtools)

Loading required package: usethis

library(ggplot2)
library(tsfeatures)

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library(class)
library(cvTools)

Loading required package: lattice
Loading required package: robustbase

library(randomForest)

randomForest 4.7-1
Type rfNews() to see new features/changes/bug fixes.

Attaching package: ‘randomForest’

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library(GEOquery) 

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Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

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Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

library(R.utils)

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library(reshape2)

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library(limma)

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library(dplyr)
library(e1071)
library(DT)

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library(viridis)

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library(plotly)

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library(scales)

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gse36059 = getGEO("GSE36059")[[1]]

Found 1 file(s)
GSE36059_series_matrix.txt.gz
|--------------------------------------------------|
|==================================================|

gse48581 = getGEO("GSE48581")[[1]]

Found 1 file(s)
GSE48581_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz 

gse129166 = getGEO("GSE129166")[[1]]

Found 1 file(s)
GSE129166_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz 

gse15296 = getGEO("GSE15296")[[1]]

Found 1 file(s)
GSE15296_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz 

gse36074_f = fData(gse36059)
gse36074_f

gse36074_f = fData(gse48581)
gse36074_f

gse129166_f = fData(gse129166)
gse129166_f

gse15296_f = fData(gse15296)
gse15296_f

gse36074_p = pData(gse36059)
gse36074_p

gse48581_p = pData(gse48581)
gse48581_p

gse129166_p = pData(gse129166)
gse129166_p

gse15296_p = pData(gse15296)
gse15296_p

data.frame(ifelse(gse36074_p$characteristics_ch1) == "diagnosis: non-rejecting", 0, 1)

Main outcomes are non-rejecting, TCMR (acute T-cell–mediated rejection), ABMR (anti-donor antibody-mediated rejection), and MIXED. Also has nephrectomy.

gse36074_ex = data.frame(t(exprs(gse36059)))
gse36074_ex

gse48581_ex = data.frame(t(exprs(gse48581)))
gse48581_ex

gse129166_ex = data.frame(t(exprs(gse129166)))
gse129166_ex

gse15296_ex = data.frame(t(exprs(gse15296)))
gse15296_ex

start = 1
stop = 100
boxplot(gse36074_ex[start:stop])

boxplot(gse48581_ex[start:stop])

boxplot(gse129166_ex[start:stop])

boxplot(gse15296_ex[start:stop])

merge(gse36074_ex, gse48581_ex, all = TRUE)